|
| Status |
Public on Jan 12, 2022 |
| Title |
Bmp2 knock out for 48h |
| Sample type |
SRA |
| |
|
| Source name |
mouse dental papilla cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Bmp2 KO
tissue: mouse dental papilla cells
culture time: 48h
|
| Treatment protocol |
Total RNA was isolated from the dental papilla Bmp2 floxed and knock out cells and Samples were subjected to RNA seq analysis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples about 1-2 mg were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
dental papilla Bmp2 knockout cells
|
| Data processing |
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were mapped to genome UCSC mm9 using TopHat v2.0.8b
Gene and Long_noncoding region count measurements were obtained using HTSeq-count based on refseq and gencode.mouse.v1.long_noncoding annotation
Genome_build: mm9-UCSC-Mus_musculus
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene/long_noncoding symbols and the second column contains the read counts of the gene/long_noncoding region using htseq-count
|
| |
|
| Submission date |
May 13, 2021 |
| Last update date |
Jan 12, 2022 |
| Contact name |
YI ZOU |
| E-mail(s) |
zou@uthscsa.edu
|
| Organization name |
UTHSA-GCCRI
|
| Street address |
8403 Floyd Curl Drive
|
| City |
SAN ANTONIO |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE174429 |
Differential LncRNA/mRNA expression profiling and functional network analyses in BMP2 deletion of mouse dental papilla cells |
|
| Relations |
| BioSample |
SAMN19168245 |
| SRA |
SRX10875377 |
